Eosinophilic esophagitis (EoE) is a significant source of morbidity in both children and adults. Currently, the clinical diagnosis of the disease is based on the correlation of clinical and histological findings. The evaluation of hematoxylin and eosin stained tissue sections relies heavily on morphologic features that overlap with those of gastroesophageal reflux disease (GERD). The clinical signs and symptoms are non-specific and also overlap significantly with those of GERD, and thus differentiating between the two diseases is one of the primary challenges in caring for patients with EoE. There is a need for a method to more specifically diagnose EoE and differentiate between GERD and EoE. The present invention addresses these needs.